Adhya / Garges RNA Polymerase and Associated Factors, Part C

1. Auflage 2003
ISBN: 978-0-08-052259-3
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band Volume 370, 789 Seiten, Web PDF

Reihe: Methods in Enzymology

RNA polymerase is molecule important to gene transcription. Along with associated factors, RNA polymerase is part of the process in which RNA is transcribed to produce a protein.* Construction and purification of RNA polymerases* DNA microarrays and bacterial gene expression* Functional analysis of transcription factors

Autoren/Hrsg.

Adhya, Sankar

Garges, Susan

Inhaltsverzeichnis

1;Cover;1
2;Title Page;4
3;Copyright Page;5
4;Table of Contents;6
5;Contributors to Volume 370;12
6;Preface;20
7;Volumes in Series;22
8;Section I: RNA Polymerase Structure and Properties;44
8.1;Chapter 1. Construction, Purification, and Characterization of Escherichia coli RNA Polymerases Tagged with Different Fluorescent Proteins;46
8.2;Chapter 2. Purification of Bacillus subtilis Polymerase and Associated Factors;53
8.3;Chapter 3. Determination of Escherichia coli RNA Polymerase Structure by Single Particle Cryoelectron Microscopy;67
8.4;Chapter 4. Crystallographic Analysis of Thermus aquaticus RNA Polymerase Holoenzyme and a Holoenzyme/Promoter DNA Complex;85
8.5;Chapter 5. Purification of Rhodobacter sphaeroides RNA Polymerase and Its Sigma Factors;97
8.6;Chapter 6. In Vitro Transcription Assays Using Components from Methanothermobacter thermautotrophicus;109
8.7;Chapter 7. Isolation and Characterization of Streptomyces coelicolor RNA Polymerase, Its Sigma, and Antisigma Factors;116
8.8;Chapter 8. Bacteriophage N4-Coded, Virion- Encapsulated DNA-Dependent RNA Polymerase;126
8.9;Chapter 9. Preparation and Characterization of Recombinant Thermus aquatics RNA Polymerase;137
8.10;Chapter 10. Purification and Assay of Upstream Activation Factor, Core Factor, Rrn3p, and Yeast RNA Polymerase I;152
8.11;Chapter 11. Purification and Transcriptional Analysis of RNA Polymerase I Holoenzymes from Broccoli (Brassica oleracea) and Frog (Xenopus laevis);164
8.12;Chapter 12. Assays and Affinity Purification of Biotinylated and Nonbiotinylated Forms of Double-Tagged Core RNA Polymerase II from Saccharomyces cerevisiae;181
8.13;Chapter 13. Dephosphorylation of the Carboxyl-Terminal Domain of RNA Polymerase II;198
8.14;Chapter 14. RNA Polymerase III from the Fission Yeast, Schizosaccharomyces pombe;208
8.15;Chapter 15. Purification of Highly-Active and Soluble Escherichia coli 70 Polypeptide Overproduced at Low Temperature;217
8.16;Chapter 16. Expression, Purification of, and Monoclonal Antibodies to Factors from Escherichia coli;224
8.17;Chapter 17. Studying Sigma–Core Interactions in Escherichia coli RNA Polymerase by Electrophoretic Shift Assays and Luminescence Resonance Energy Transfer;235
8.18;Chapter 18. Assay of Escherichia coli RNA Polymerase: Sigma–Core Interactions;249
8.19;Chapter 19. Purification and Characterization of Bacteriophage-Encoded Inhibitors of Host RNA Polymerase: T-Odd Phage gp2-like Proteins;255
9;Section II: Analyses of Promoter and Transcription Patterns;270
9.1;Chapter 20. A Procedure for Identifying Loosely Conserved Protein-Binding DNA Sequences;272
9.2;Chapter 21. Computational Detection of Vertebrate RNA Polymerase II Promoters;280
9.3;Chapter 22. Detection of DNA-Binding Helix-Turn-Helix Motifs in Proteins Using the Pattern Dictionary Method;293
9.4;Chapter 23. DNA Microarrays and Bacterial Gene Expression;307
9.5;Chapter 24. Analysis of Microarray Data for the marA, soxS, and rob Regulons of Escherichia coli;321
10;Section III: Polymerase Associated Factors;324
10.1;Chapter 25. Purification and Activity Assays of RapA, the RNA Polymerase-Associated Homolog of the SWI/SNF Protein Superfamily;326
10.2;Chapter 26. Escherichia coli Proteins Eluted from Mono Q Chromatography, a Final Step During RNA Polymerase Purification Procedure;334
10.3;Chapter 27. Techniques for Studying the Oxygen-Sensitive Transcription Factor FNR from Escherichia coli;343
10.4;Chapter 28. Assay of Transcription Modulation by Spo0A of Bacillus subtilis;355
10.5;Chapter 29. Assay of Prokaryotic Enhancer Activity over a Distance In Vitro;367
10.6;Chapter 30. DnaA as a Transcription Regulator;381
10.7;Chapter 31. Analysis of Transcription Factor Interactions at Sedimentation Equilibrium;392
10.8;Chapter 32. Single-Molecule Studies of DNA Architectural Changes Induced by Regulatory Proteins;412
10.9;Chapter 33. Assay of an Intrinsic Acetyltransferase Activity of the Transcriptional Coactivator CIITA;421
10.10;Chapter 34. Purification and Assay of Saccharomyces cerevisiae Phosphatase That Acts on the C-Terminal Domain of the Largest Subunit of RNA Polymerase II;429
10.11;Chapter 35. Functional Analysis of Transcription Factors CREB and CREM;439
10.12;Chapter 36. Functional Analysis of TFIID Components Using Conditional Mutants;458
10.13;Chapter 37. Immunoaffinity Purification of Mammalian Protein Complexes;473
10.14;Chapter 38. Interaction of Gal4p with Components of Transcription Machinery In Vivo;488
10.15;Chapter 39. Dominant-Negative Mutants of Helix-Loop- Helix Proteins: Transcriptional Inhibition;497
10.16;Chapter 40. Purification and Transcription Repression by Negative Cofactor 2;510
10.17;Chapter 41. Hap1p Photofootprinting as an In Vivo Assay of Repression Mechanism in Saccharomyces;522
10.18;Chapter 42. Analysis of Activator-Dependent Transcription Reinitiation In Vitro;530
11;Section IV: Transcription Initiation;546
11.1;Chapter 43. Molecular Analysis of Activator Engagement with RNA Polymerase;548
11.2;Chapter 44. Purification and Protein Interaction Assays of the VP16C Transcription Activation Domain;565
11.3;Chapter 45. Rapid Quench Mixing to Quantify Kinetics of Steps in Association of Escherichia coli RNA Polymerase with Promoter DNA;578
11.4;Chapter 46. Determination of RNA Polymerase Binding and Isomerization Parameters by Measuring Abortive Initiations;589
11.5;Chapter 47. Probing the Role of Region 2 of Escherichia coli 70 in the Nucleation and Maintenance of the Single-Stranded DNA Bubble in RNA Polymerase-Promoter Open Complexes;596
11.6;Chapter 48. On the Use of 2-Aminopurine as a Probe for Basepair Opening During Transcription Initiation;611
11.7;Chapter 49. Single-Molecule DNA Nanomanipulation: Detection or Promoter-Unwinding Events by RNA Polymerase;620
11.8;Chapter 50. Simple Fluorescence Assays Probing Conformational Changes of Escherichia coli RNA Polymerase During Transcription Initiation;641
11.9;Chapter 51. Measuring Control of Transcription Initiation by Changing Concentrations of Nucleotides and Their Derivatives;649
11.10;Chapter 52. Identification of Promoters of Escherichia coli and Phage in the Transcription Section Plasmid pSA508;661
11.11;Chapter 53. Enhancer-Dependent Transcription by Bacterial RNA Polymerase: The Subunit Downstream Lobe Is Used by 54 During Open Promoter Complex Formation;689
11.12;Chapter 54. Mutational Analysis and Structure of the Phage SP6 Promoter;701
11.13;Chapter 55. Fluorescence Methods for Studying the Kinetics and Thermodynamics of Transcription Initiation;711
11.14;Chapter 56. In Vitro Studies of the Early Steps of RNA Synthesis by Human RNA Polymerase II;730
11.15;Chapter 57. Site-Specific Protein-DNA Photocross-Linking of Purified Complexes: Topology of the RNA Polymerase II Transcription Initiation Complex;744
11.16;Chapter 58. Assay of Promoter Melting and Extension of mRNA: Role of TFIIH Subunits;756
11.17;Chapter 59. Assays for Investigating the Mechanism of Promoter Escape by RNA Polymerase II;776
12;Author Index;784
13;Subject Index;816